@@ -38,6 +38,7 @@
#:use-module (gnu packages netpbm)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
+ #:use-module (gnu packages protobuf)
#:use-module (gnu packages statistics)
#:use-module (gnu packages web)
#:use-module (srfi srfi-1))
@@ -6166,3 +6167,33 @@ data.")
(synopsis "Visualization for flow cytometry data")
(description "This package provides visualization tools for flow cytometry data.")
(license license:artistic2.0)))
+
+(define-public r-rprotobuflib
+ (package
+ (name "r-rprotobuflib")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RProtoBufLib" version))
+ (sha256
+ (base32
+ "1vhwxw7281n5wpg30ik3m1gwarfmj4b8cqxdvj0sck44yx24lphg"))
+ ;; Remove bundled binaries:
+ ;; src/win/lib/{i386,x64}/libprotobuf.a
+ (modules '((guix build utils)))
+ (snippet '(begin
+ (delete-file-recursively "src/win")
+ #t))
+ (patches
+ (search-patches "r-rprotobuflib-unbundle-dependency.patch"))))
+ (properties
+ `((upstream-name . "RProtoBufLib")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("protobuf-2" ,protobuf-2)))
+ (home-page "https://bioconductor.org/packages/RProtoBufLib")
+ (synopsis "C++ headers and static libraries of Protocol buffers")
+ (description "This package provides the headers and static library of
+Protocol buffers for other R packages to compile and link against.")
+ (license license:bsd-3)))
new file mode 100644
@@ -0,0 +1,57 @@
+diff --git a/configure b/configure
+index 7edae5f..eff2489 100755
+--- a/configure
++++ b/configure
+@@ -2856,39 +2856,6 @@ ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ex
+ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+
+-#untar the lib
+-BASEPBNAME="protobuf-2.6.0"
+-PBTGZNAME=${BASEPBNAME}.tgz
+-cd src
+-if test -d ./${BASEPBNAME}; then
+- echo 'found ' $BASEPBNAME ' header sources and tar archive;using what is there.'
+-else
+- echo "untarring protobuf ...";
+- gunzip -dc ${PBTGZNAME} | tar xf -;
+-fi;
+-
+-#run this bootstrap script to update all the gnu auto build files (e.g. automake symlinked fils (e.g. ./compile), alocal.m4,etc... )
+-cd ${BASEPBNAME}
+-#./autogen.sh
+-#automake --add-missing #do this because the old Autoconf (e.g. 2.13) may not handle this in autoreconf
+-#mv m4/lt~obsolete.m4 m4/lt-obsolete.m4 # R CMD check gives warning about ~ character in filename
+-cd ..
+-
+-echo "building protobuf...";
+-PBBUILD=$(pwd)/pb_build
+-if test -d ${PBBUILD}; then
+- echo 'found ' $PBBUILD ' ;using what is there.'
+-else
+- mkdir ${PBBUILD}
+-fi;
+-
+-cd ${BASEPBNAME};
+-./configure --enable-static=yes --with-pic=yes --enable-shared=no --prefix="${PBBUILD}" --libdir="${PBBUILD}/lib" CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" CC="${CC}" CFLAGS="${CFLAGS}"
+-$MAKE install
+-
+-cd ../../
+-
+-
+
+
+ ac_config_files="$ac_config_files src/Makevars"
+diff --git a/src/Makevars.in b/src/Makevars.in
+index 63803fb..575d507 100644
+--- a/src/Makevars.in
++++ b/src/Makevars.in
+@@ -10,9 +10,6 @@ all: copying
+
+ #copy hdf5 library headers to package include
+ copying: $(GS_LIB)
+- mkdir -p "${USER_INCLUDE}"
+- cp -r @PBBUILD@/include/google ${USER_INCLUDE}
+ mkdir -p "${USER_LIB_DIR}"
+- cp @PBBUILD@/lib/* ${USER_LIB_DIR}
+ cp $(GS_LIB) ${USER_LIB_DIR}/GatingSet.pb.o